This article addresses the pressing issue of pest outbreaks in India, which poses significant challenges for farmers and ecologists. A novel system is proposed for effective control that leverages natural enemies. Here, the pests are classified into juveniles and mature individuals, further categorized as susceptible or infected. The study introduces harvesting, incorporating external efforts and natural phenomena, in a pest-epidemic prey–predator system featuring a prey-stage structure. The model reveals three equilibria: trivial, boundary (indicating the absence of natural enemies), and interior equilibria. Notably, the trivial equilibrium is consistently unstable. As demonstrated by stability analysis, the survival or extinction of natural enemies hinges on control variables, including the harvesting rate, disease transmission rate, and natural death rate. Local stability is assessed using the Routh–Hurwitz criterion, while global stability is explored through the Lyapunov method. Furthermore, optimal control theory and Pontryagin’s maximum principle are applied for model optimization, unveiling crucial optimality conditions and determining the optimal harvesting rate for susceptible mature prey. Numerical computations validate theoretical insights, offering valuable guidance for formulating policies that optimize the control of susceptible adult pests within a disease-induced pest-natural enemy system, ensuring sustained cost-effectiveness.